Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
A searchable table of the S. cerevisiae pangenome ORFs defined in Peter et al. (2018) Nature (LINK) is provided below. The listed core/accessory classification and origin assignment are based on the original study. Click on the PanORF ID to find out the detailed presence/absence pattern of the corresponding pangenome ORF in both ScRAPdb and the 1002ScGP strain collections (which were recalculated by ScRAPdb).
| PanORF ID | SGD systematic Name | SGD standard name | Alias | Description | Type | Origin assignment | Mostly likely origin species | NCBI megablast hit |
|---|---|---|---|---|---|---|---|---|
| 5918-YLR466C-B | YLR466C-B | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Unknown | S. paradoxus | NA |
| 5919-YLR467W_NumOfGenes_63 | YLR467W | YRF1-5 | Y' element ATP-dependent helicase protein 1 copy 5|YRF1 | Helicase encoded by the Y' element of subtelomeric regions; highly expressed in the mutants lacking the telomerase component TLC1; potentially phosphorylated by Cdc28p | Accessory | Introgression | S. paradoxus | NA |
| 5920-YML001W | YML001W | YPT7 | Rab family GTPase YPT7|VAM4|AST4 | Rab family GTPase; GTP-binding protein of the rab family; required for homotypic fusion event in vacuole inheritance, for endosome-endosome fusion; localizes to sites of contact between the vacuole and mitochondria (vCLAMPs); interacts with the cargo selection/retromer complex for retrograde sorting; similar to mammalian Rab7 | Core | NA | NA | NA |
| 5921-YML002W | YML002W | NA | NA | Putative protein of unknown function; expression induced by heat and by calcium shortage | Core | NA | NA | NA |
| 5922-YML003W | YML003W | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 5923-YML004C | YML004C | GLO1 | lactoylglutathione lyase GLO1 | Monomeric glyoxalase I; catalyzes the detoxification of methylglyoxal (a by-product of glycolysis) via condensation with glutathione to produce S-D-lactoylglutathione; expression regulated by methylglyoxal levels and osmotic stress | Accessory | Ancestral | NA | NA |
| 5924-YML005W | YML005W | TRM12 | TYW2 | S-adenosylmethionine-dependent methyltransferase; required for wybutosine formation in phenylalanine-accepting tRNA; member of the seven beta-strand family | Accessory | Ancestral | NA | NA |
| 5925-YML006C | YML006C | GIS4 | NA | CAAX box containing protein of unknown function; proposed to be involved in the RAS/cAMP signaling pathway | Core | NA | NA | NA |
| 5926-YML007C-A | YML007C-A | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to mitochondria | Core | NA | NA | NA |
| 5927-YML007W | YML007W | YAP1 | PDR4|DNA-binding transcription factor YAP1|SNQ3|PAR1 | Basic leucine zipper (bZIP) transcription factor; required for oxidative stress tolerance; activated by H2O2 through the multistep formation of disulfide bonds and transit from the cytoplasm to the nucleus; Yap1p is degraded in the nucleus after the oxidative stress has passed; mediates resistance to cadmium; relative distribution to the nucleus increases upon DNA replication stress; YAP1 has a paralog, CAD1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5928-YML008C | YML008C | ERG6 | sterol 24-C-methyltransferase|VID1|SED6|LIS1|ISE1 | Delta(24)-sterol C-methyltransferase; converts zymosterol to fecosterol in the ergosterol biosynthetic pathway by methylating position C-24; localized to lipid particles, the plasma membrane-associated endoplasmic reticulum, and the mitochondrial outer membrane | Core | NA | NA | NA |
| 5929-YML009C | YML009C | MRPL39 | mitochondrial 54S ribosomal protein YmL39|YmL39 | Mitochondrial ribosomal protein of the large subunit | Core | NA | NA | NA |
| 5930-YML009C-A | YML009C-A | NA | YML010W-B|YML010C-B | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps ORFs SPT5/YML010W and YML009W-B | Accessory | Unknown | NA | NA |
| 5931-YML010W_NumOfGenes_2 | YML010W | SPT5 | transcription elongation factor SPT5 | Spt4p/5p (DSIF) transcription elongation factor complex subunit; the Spt4/5 complex binds to ssRNA in a sequence-specific manner, and in concert with RNAP I and II has multiple roles regulating transcriptional elongation, RNA processing, quality control, and transcription-coupled repair; interacts with DNA upstream of RNAPII and the non-template strand of the transcription bubble; Spt5p is the only transcription elongation factor conserved in all domains of life | Core | NA | NA | NA |
| 5932-YML011C | YML011C | RAD33 | NA | Protein involved in nucleotide excision repair; green fluorescent protein (GFP)-fusion protein localizes to the nucleus | Core | NA | NA | NA |